readsDistribution {ribosomeProfilingQC} | R Documentation

## Plot reads distribution in genomic elements

### Description

Plot the percentage of reads in CDS, 5'UTR, 3'UTR, introns, and other elements.

### Usage

    readsDistribution(
      reads,
      txdb,
      upstreamRegion = 3000,
      downstreamRegion = 3000,
      plot = TRUE,
      ...
    )

### Arguments

`reads` | Output of getPsiteCoordinates
`txdb` | A TxDb object
`upstreamRegion, downstreamRegion` | The range for promoter region and downstream region.
`plot` | Plot the distribution or not
`...` | Not use.

### Value

The reads with distribution assignment

### Examples

    library(Rsamtools)
    bamfilename <- system.file("extdata", "RPF.WT.1.bam",
                               package="ribosomeProfilingQC")
    yieldSize <- 10000000
    bamfile <- BamFile(bamfilename, yieldSize = yieldSize)
    pc <- getPsiteCoordinates(bamfile, bestpsite=11)
    pc.sub <- pc[pc$qwidth %in% c(29, 30)]
    library(GenomicFeatures)
    library(BSgenome.Drerio.UCSC.danRer10)
    txdb <- makeTxDbFromGFF(system.file("extdata",
              "Danio_rerio.GRCz10.91.chr1.gtf.gz",
              package="ribosomeProfilingQC"),
              organism = "Danio rerio",
              chrominfo = seqinfo(Drerio)["chr1"],
              taxonomyId = 7955)
    pc.sub <- readsDistribution(pc.sub, txdb, las=2)

[Package ribosomeProfilingQC version 0.99.9 Index]